figures
rm(list = ls(all.names = TRUE))
library(ggplot2)
library(tidyr)
library(dplyr)
library(knitr)
library(rmarkdown)
library(formatR)data <- read.csv("df/icer-all.csv", as.is = TRUE)
df <- data[(data$scenario!="base"),]
df$cases.averted <- as.numeric(df$cases.averted)
df$cases.averted.per100k <- as.numeric(df$cases.averted.per100k)
df$icer.case.averted <- as.numeric(df$icer.case.averted)
df$deaths.averted <- as.numeric(df$deaths.averted)
df$deaths.averted.per100k <- as.numeric(df$ deaths.averted.per100k)
df$icer.death.averted <- as.numeric(df$icer.death.averted)
df$dalys <- as.numeric(df$dalys)
df$dalys.per100k <- as.numeric(df$dalys.per100k)
df$dalys.averted <- as.numeric(df$dalys.averted)
df$dalys.averted.per100k <- as.numeric(df$dalys.averted.per100k)
df$icer.daly.averted <- as.numeric(df$icer.daly.averted)# subset relevant efficacies
df2 <- df[!(df$scenario == 'vaxbase' & df$v.eff %in% c(50, 60)),]
#table(df2$v.eff, useNA = 'always')
df3 <- df2[!(df2$scenario == 'vax70' & df2$v.eff %in% c(30,40)), ]
#table(df3$scenario, df3$v.eff, useNA = 'always')
# factors
df3$age <- factor(df3$age, levels = c("0-4 yrs", "5-19 yrs", "20-64 yrs", "65+ yrs", "All"))
df3$risk <- factor(df3$risk, levels = c("High", "Non-high", "All"))
df3$scenario <- factor(df3$scenario, levels = c("vaxbase", "vax70"))
df3$v.eff <- factor(df3$v.eff)1 Tables
Subset data.
# subset scenario
df_base <- df3[(df3$scenario == 'vaxbase'),]
df_vax70 <- df3[(df3$scenario == 'vax70'),]
# age groups
age_df_base <- df_base[(df_base$risk == "All"),]
age_df_vax70 <- df_vax70[(df_vax70$risk == "All"),]
# risk groups
risk_df_base <- df_base[!(df_base$age == 'All'),]
risk_df_vax70 <- df_vax70[!(df_vax70$age == 'All'),]2 Base Vaccination Scenario
2.1 Fig. ICER per case averted
ggplot(age_df_base, aes(x = age, y = icer.case.averted, color = v.eff, group = v.eff)) +
geom_point() + geom_line(linetype = "dotted") + labs(x = "Age group", color = "Vaccine \nefficacy") +
ylab("$ saved per case averted") + ggtitle("Base Vaccination: ICER per case averted")
ggplot(df_base[(df_base$age == "All"), ], aes(x = v.eff, y = icer.case.averted,
group = risk, color = risk)) + geom_point() + geom_line(linetype = "dotted") +
labs(x = "Vaccine efficacy (%)", color = "Risk") + ylab("$ saved per case averted") +
ggtitle("Base Vaccination: ICER per case averted")
ggplot(df_base, aes(x = age, y = icer.case.averted, group = risk, color = risk)) +
geom_point() + geom_line(linetype = "dotted") + labs(x = "Age group", color = "Risk group") +
ylab("$ saved per case averted") + ggtitle("Base Vaccination: ICER per case averted") +
facet_grid(~v.eff)
2.2 Fig. ICER per death averted
ggplot(age_df_base, aes(x = age, y = icer.death.averted, color = v.eff, group = v.eff)) +
geom_point() + geom_line(linetype = "dotted") + labs(x = "Age group", color = "Vaccine \nefficacy") +
ylab("$ saved per death averted") + ggtitle("Base Vaccination: ICER per death averted")
ggplot(df_base[(df_base$age == "All"), ], aes(x = v.eff, y = icer.death.averted,
group = risk, color = risk)) + geom_point() + geom_line(linetype = "dotted") +
labs(x = "Vaccine efficacy (%)", color = "Risk") + ylab("$ saved per death averted") +
ggtitle("Base Vaccination: ICER per death averted")
ggplot(df_base, aes(x = age, y = icer.death.averted, group = risk, color = risk)) +
geom_point() + geom_line(linetype = "dotted") + labs(x = "Age group", color = "Risk group") +
ylab("$ saved per death averted") + ggtitle("Base Vaccination: ICER per death averted") +
facet_grid(~v.eff)
2.3 Fig. ICER per DALY averted
ggplot(age_df_base, aes(x = age, y = icer.daly.averted, color = v.eff, group = v.eff)) +
geom_point() + geom_line(linetype = "dotted") + labs(x = "Age group", color = "Vaccine \nefficacy") +
ylab("$ saved per DALY averted") + ggtitle("Base Vaccination: ICER per DALY averted")
ggplot(df_base[(df_base$age == "All"), ], aes(x = v.eff, y = icer.daly.averted,
group = risk, color = risk)) + geom_point() + geom_line(linetype = "dotted") +
labs(x = "Vaccine efficacy (%)", color = "Risk") + ylab("$ saved per DALY averted") +
ggtitle("Base Vaccination: ICER per DALY averted")
ggplot(df_base, aes(x = age, y = icer.daly.averted, group = risk, color = risk)) +
geom_point() + geom_line(linetype = "dotted") + labs(x = "Age group", color = "Risk group") +
ylab("$ saved per DALY averted") + ggtitle("Base Vaccination: ICER per DALY averted") +
facet_grid(~v.eff)
Set up plots.
# age
g1 <- ggplot(age_df_base, aes(x = age, group = v.eff, color = v.eff)) + geom_point() +
geom_line(linetype = "dotted") + labs(x = "Age group", color = "Vaccine \nefficacy")
# risk
g2 <- ggplot(df_base[(df_base$age == "All"), ], aes(x = v.eff, group = risk,
color = risk)) + geom_point() + geom_line(linetype = "dotted") + labs(x = "Vaccine efficacy",
color = "Risk group")
g3 <- ggplot(risk_df_base, aes(x = age, group = risk, color = risk)) + geom_point() +
geom_line(linetype = "dotted") + labs(x = "Age group", color = "Risk group") +
facet_grid(~v.eff)2.4 Fig. Cases, cases averted
# age groups
g1 + aes(y = cases) + labs(y = "Cases", title = "Base Vaccination: Cases")
g1 + aes(y = cases.per100k) + labs(y = "Cases per 100k", title = "Base Vaccination: Cases per 100k")
g1 + aes(y = cases.averted) + labs(y = "Cases averted", title = "Base Vaccination: Cases averted")
g1 + aes(y = cases.averted.per100k) + labs(y = "Cases averted per 100k", title = "Base Vaccination: Cases averted per 100k")
# risk groups
g2 + aes(y = cases) + labs(y = "Cases", title = "Base Vaccination: Cases")
g2 + aes(y = cases.per100k) + labs(y = "Cases per 100k", title = "Base Vaccination: Cases per 100k")
g2 + aes(y = cases.averted) + labs(y = "Cases averted", title = "Base Vaccination: Cases averted")
g2 + aes(y = cases.averted.per100k) + labs(y = "Cases averted per 100k", title = "Base Vaccination: Cases averted per 100k")
g3 + aes(y = cases) + labs(y = "Cases", title = "Base Vaccination: Cases")
g3 + aes(y = cases.per100k) + labs(y = "Cases per 100k", title = "Base Vaccination: Cases per 100k")
g3 + aes(y = cases.averted) + labs(y = "Cases averted", title = "Base Vaccination: Cases averted")
g3 + aes(y = cases.averted.per100k) + labs(y = "Cases averted per 100k", title = "Base Vaccination: Cases averted per 100k")
2.5 Fig. Deaths, deaths averted
# age groups
g1 + aes(y = deaths) + labs(y = "Deaths", title = "Base Vaccination: Deaths")
g1 + aes(y = deaths.per100k) + labs(y = "Deaths per 100k", title = "Base Vaccination: Deaths per 100k")
g1 + aes(y = deaths.averted) + labs(y = "Deaths averted", title = "Base Vaccination: Deaths averted")
g1 + aes(y = deaths.averted.per100k) + labs(y = "Deaths averted per 100k", title = "Base Vaccination: Deaths averted per 100k")
# risk groups
g2 + aes(y = deaths) + labs(y = "Deaths", title = "Base Vaccination: Deaths")
g2 + aes(y = deaths.per100k) + labs(y = "Deaths per 100k", title = "Base Vaccination: Deaths per 100k")
g2 + aes(y = deaths.averted) + labs(y = "Deaths averted", title = "Base Vaccination: Deaths averted")
g2 + aes(y = deaths.averted.per100k) + labs(y = "Deaths averted per 100k", title = "Base Vaccination: Deaths averted per 100k")
g3 + aes(y = deaths) + labs(y = "Deaths", title = "Base Vaccination: Deaths")
g3 + aes(y = deaths.per100k) + labs(y = "Deaths per 100k", title = "Base Vaccination: Deaths per 100k")
g3 + aes(y = deaths.averted) + labs(y = "Deaths averted", title = "Base Vaccination: Deaths averted")
g3 + aes(y = deaths.averted.per100k) + labs(y = "Deaths averted per 100k", title = "Base Vaccination: Deaths averted per 100k")
2.6 Fig. DALYs, DALYs averted
# age groups
g1 + aes(y = dalys) + labs(y = "DALYs", title = "Base Vaccination: DALYs")
g1 + aes(y = dalys.per100k) + labs(y = "DALYs per 100k", title = "Base Vaccination: DALYs per 100k")
g1 + aes(y = dalys.averted) + labs(y = "DALYs averted", title = "Base Vaccination: DALYs averted")
g1 + aes(y = dalys.averted.per100k) + labs(y = "DALYs averted per 100k", title = "Base Vaccination: DALYs averted per 100k")
# risk groups
g2 + aes(y = dalys) + labs(y = "DALYs", title = "Base Vaccination: DALYs")
g2 + aes(y = dalys.per100k) + labs(y = "DALYs per 100k", title = "Base Vaccination: DALYs per 100k")
g2 + aes(y = dalys.averted) + labs(y = "DALYs averted", title = "Base Vaccination: DALYs averted")
g2 + aes(y = dalys.averted.per100k) + labs(y = "DALYs averted per 100k", title = "Base Vaccination: DALYs averted per 100k")
g3 + aes(y = dalys) + labs(y = "DALYs", title = "Base Vaccination: DALYs")
g3 + aes(y = dalys.per100k) + labs(y = "DALYs per 100k", title = "Base Vaccination: DALYs per 100k")
g3 + aes(y = dalys.averted) + labs(y = "DALYs averted", title = "Base Vaccination: DALYs averted")
g3 + aes(y = dalys.averted.per100k) + labs(y = "DALYs averted per 100k", title = "Base Vaccination: DALYs averted per 100k")
3 70% Vaccination Scenario
3.1 Fig. ICER per case averted
g <- ggplot(df_vax70[(df_vax70$age == "All"), ], aes(x = v.eff, color = risk,
group = risk))
t1 <- labs(y = "$ saved per case averted", title = "70% Vaccination: ICER per case averted")
t2 <- labs(y = "$ saved per death averted", title = "70% Vaccination: ICER per death averted")
t3 <- labs(y = "$ saved per DALY averted", title = "70% Vaccination: ICER per DALY averted")
ggplot(age_df_vax70, aes(x = age, y = icer.case.averted, color = v.eff, group = v.eff)) +
geom_point() + geom_line(linetype = "dotted") + labs(x = "Age group", color = "Vaccine \nefficacy") +
t1
g + aes(y = icer.case.averted) + geom_point() + geom_line(linetype = "dotted") +
t1 + labs(x = "Vaccine efficacy (%)", color = "Risk group")
ggplot(df_vax70, aes(x = age, y = icer.case.averted, group = risk, color = risk)) +
geom_point() + geom_line(linetype = "dotted") + labs(color = "Risk group") +
ylab("$ saved per case averted") + ggtitle("70% Vaccination: ICER per case averted") +
facet_grid(~v.eff)
3.2 Fig. ICER per death averted
ggplot(age_df_vax70, aes(x = age, y = icer.death.averted, color = v.eff, group = v.eff)) +
geom_point() + geom_line(linetype = "dotted") + labs(x = "Age group", color = "Vaccine \nefficacy") +
t2
g + aes(y = icer.death.averted) + geom_point() + geom_line(linetype = "dotted") +
t2 + labs(x = "Vaccine efficacy (%)", color = "Risk group")
ggplot(df_vax70, aes(x = age, y = icer.death.averted, group = risk, color = risk)) +
geom_point() + geom_line(linetype = "dotted") + labs(color = "Risk group") +
ylab("$ saved per death averted") + ggtitle("70% Vaccination: ICER per death averted") +
facet_grid(~v.eff)
3.3 Fig. ICER per DALY averted
ggplot(age_df_vax70, aes(x = age, y = icer.daly.averted, color = v.eff, group = v.eff)) +
geom_point() + geom_line(linetype = "dotted") + labs(x = "Age group", color = "Vaccine \nefficacy") +
t3
g + aes(y = icer.daly.averted) + geom_point() + geom_line(linetype = "dotted") +
t3 + labs(x = "Vaccine efficacy (%)", color = "Risk group")
ggplot(df_vax70, aes(x = age, y = icer.daly.averted, group = risk, color = risk)) +
geom_point() + geom_line(linetype = "dotted") + labs(color = "Risk group") +
ylab("$ saved per DALY averted") + ggtitle("70% Vaccination: ICER per DALY averted") +
facet_grid(~v.eff)
Set up plots.
# age
h1 <- ggplot(age_df_vax70, aes(x = age, group = v.eff, color = v.eff)) + geom_point() +
geom_line(linetype = "dotted") + labs(x = "Age group", color = "Vaccine \nefficacy")
# risk
h2 <- ggplot(df_vax70[(df_vax70$age == "All"), ], aes(x = v.eff, group = risk,
color = risk)) + geom_point() + geom_line(linetype = "dotted") + labs(x = "Vaccine efficacy",
color = "Risk group")
h3 <- ggplot(risk_df_vax70, aes(x = age, group = risk, color = risk)) + geom_point() +
geom_line(linetype = "dotted") + labs(x = "Age group", color = "Risk group") +
facet_grid(~v.eff)3.4 Fig. Cases, cases averted
# age groups
h1 + aes(y = cases) + labs(y = "Cases", title = "70% Vaccination: Cases")
h1 + aes(y = cases.per100k) + labs(y = "Cases per 100k", title = "70% Vaccination: Cases per 100k")
h1 + aes(y = cases.averted) + labs(y = "Cases averted", title = "70% Vaccination: Cases averted")
h1 + aes(y = cases.averted.per100k) + labs(y = "Cases averted per 100k", title = "70% Vaccination: Cases averted per 100k")
# risk groups
h2 + aes(y = cases) + labs(y = "Cases", title = "70% Vaccination: Cases")
h2 + aes(y = cases.per100k) + labs(y = "Cases per 100k", title = "70% Vaccination: Cases per 100k")
h2 + aes(y = cases.averted) + labs(y = "Cases averted", title = "70% Vaccination: Cases averted")
h2 + aes(y = cases.averted.per100k) + labs(y = "Cases averted per 100k", title = "70% Vaccination: Cases averted per 100k")
h3 + aes(y = cases) + labs(y = "Cases", title = "70% Vaccination: Cases")
h3 + aes(y = cases.per100k) + labs(y = "Cases per 100k", title = "70% Vaccination: Cases per 100k")
h3 + aes(y = cases.averted) + labs(y = "Cases averted", title = "70% Vaccination: Cases averted")
h3 + aes(y = cases.averted.per100k) + labs(y = "Cases averted per 100k", title = "70% Vaccination: Cases averted per 100k")
3.5 Fig. Deaths, deaths averted
# age groups
h1 + aes(y = deaths) + labs(y = "Deaths", title = "70% Vaccination: Deaths")
h1 + aes(y = deaths.per100k) + labs(y = "Deaths per 100k", title = "70% Vaccination: Deaths per 100k")
h1 + aes(y = deaths.averted) + labs(y = "Deaths averted", title = "70% Vaccination: Deaths averted")
h1 + aes(y = deaths.averted.per100k) + labs(y = "Deaths averted per 100k", title = "70% Vaccination: Deaths averted per 100k")
# risk groups
h2 + aes(y = deaths) + labs(y = "Deaths", title = "70% Vaccination: Deaths")
h2 + aes(y = deaths.per100k) + labs(y = "Deaths per 100k", title = "70% Vaccination: Deaths per 100k")
h2 + aes(y = deaths.averted) + labs(y = "Deaths averted", title = "70% Vaccination: Deaths averted")
h2 + aes(y = deaths.averted.per100k) + labs(y = "Deaths averted per 100k", title = "70% Vaccination: Deaths averted per 100k")
h3 + aes(y = deaths) + labs(y = "Deaths", title = "70% Vaccination: Deaths")
h3 + aes(y = deaths.per100k) + labs(y = "Deaths per 100k", title = "70% Vaccination: Deaths per 100k")
h3 + aes(y = deaths.averted) + labs(y = "Deaths averted", title = "70% Vaccination: Deaths averted")
h3 + aes(y = deaths.averted.per100k) + labs(y = "Deaths averted per 100k", title = "70% Vaccination: Deaths averted per 100k")
3.6 Fig. DALYs, DALYs averted
# age groups
h1 + aes(y = dalys) + labs(y = "DALYs", title = "70% Vaccination: DALYs")
h1 + aes(y = dalys.per100k) + labs(y = "DALYs per 100k", title = "70% Vaccination: DALYs per 100k")
h1 + aes(y = dalys.averted) + labs(y = "DALYs averted", title = "70% Vaccination: DALYs averted")
h1 + aes(y = dalys.averted.per100k) + labs(y = "DALYs averted per 100k", title = "70% Vaccination: DALYs averted per 100k")
# risk groups
h2 + aes(y = dalys) + labs(y = "DALYs", title = "70% Vaccination: DALYs")
h2 + aes(y = dalys.per100k) + labs(y = "DALYs per 100k", title = "70% Vaccination: DALYs per 100k")
h2 + aes(y = dalys.averted) + labs(y = "DALYs averted", title = "70% Vaccination: DALYs averted")
h2 + aes(y = dalys.averted.per100k) + labs(y = "DALYs averted per 100k", title = "70% Vaccination: DALYs averted per 100k")
h3 + aes(y = dalys) + labs(y = "DALYs", title = "70% Vaccination: DALYs")
h3 + aes(y = dalys.per100k) + labs(y = "DALYs per 100k", title = "70% Vaccination: DALYs per 100k")
h3 + aes(y = dalys.averted) + labs(y = "DALYs averted", title = "70% Vaccination: DALYs averted")
h3 + aes(y = dalys.averted.per100k) + labs(y = "DALYs averted per 100k", title = "70% Vaccination: DALYs averted per 100k")